The line between viruses and parasitic elements of the genome is thin and del-icate, and probably often crossed. Para-sitic elements that acquire the means to escape the host cell become viruses and, conversely, viruses can lose this ability and return to a more limited lifestyle as transposable elements (TEs). Add hori-zontal gene exchange to the mix, and you get a tangle of evolutionary rela-tionships difficult to sort. Enter Polin-tons: large DNA transposons, typically 15 − 25 kb in length. Their wide distri-bution among eukaryotes—from fungi and trichomonads, to frogs, crocodiles, and insects—speaks to their ancient origins. Now Krupovic and Koonin demonstrate their central position in the evolution of a wide range of TEs and eukaryotic viruses.

This chapter begins with a discussion on Giardia lamblia. Recent studies document antigenic variation with surface antigen changes during human infections with G. lamblia; although the biological importance of this work is not clear, it suggests that this variation may provide a mechanism for the organism to escape the host immune response. Routine stool examinations are normally recommended for the recovery and identification of intestinal protozoa. A new and simple colorimetric method has been determined for determining in vitro activity against G. lamblia. Most experts agree that the single most effective practice that prevents the spread of infection in the child care setting is thorough handwashing by the children, staff, and visitors. Currently, the most commonly used method for examining purified material for protozoa is an antibody-based immunofluorescence assay. Isolates from asymptomatic individuals were found in the same zymodemes (isoenzyme groups) as were isolates from symptomatic hosts. The chapter next focuses on Dientamoeba fragilis. Since there is no known cyst stage, this organism will not be seen on a wet preparation. Consequently, it is mandatory that a permanent stained smear be included in the ova and parasite examination. Current recommendations include iodoquinol, paromomycin, or tetracycline. Since symptomatic relief has been observed to follow appropriate therapy, Dientamoeba fragilis is probably pathogenic in infected individuals who are symptomatic. Finally, the chapter focuses on Pentatrichomonas hominis, Chilomastix mesnili, Enteromonas hominis, Retortamonas intestinalis, and Balantidium coli.

Symptoms that have been attributed to the pinworm infection, particularly in children, include nervousness, insomnia, nightmares, and even convulsions. In some cases, perianal granulomas may result. If the amount of material limits the examination to one procedure, the use of polyvinyl alcohol (PVA) fixative is highly recommended. Many physicians performing sigmoidoscopy procedures do not realize the importance of selecting the proper fixative for material to be examined for parasites. One of the organisms most strongly suspected when sigmoidoscopy is performed is Entamoeba histolytica, whose morphology is normally seen from the permanent stained smear; however, this identification assumes that RBCs are seen within the cytoplasm of the trophozoites. Duodenal drainage material can be submitted for examination as direct or concentration wet mounts or permanent stained smears, techniques that may reveal the parasites. Examination of urinary sediment is indicated in certain filarial infections. The occurrence of microfilariae in urine has been reported with increasing frequency in Onchocerca volvulus infections in Africa. The identification of Trichomonas vaginalis is usually based on the examination of a wet preparation of vaginal and urethral discharges and prostatic secretions or urine sediment. The efficiency of the polycarbonate membrane filtration technique for detecting Schistosoma haematobium eggs in urine is increased by using a pore size of 14 μm and the suction of a water jet pump.

Although many body sites and specimens can be examined for the presence of parasites, the most difficult specimen in which to differentiate parasites from artifacts is usually fecal material. Feces consist of a number of components, including (i) undigested food residue; (ii) digestive by-products; (iii) epithelial cells, mucus, and other secretions from the digestive tract; and (iv) many types of microorganisms such as bacteria and yeasts. Considering the ratio between fecal debris and parasites, it is not surprising that many artifacts are responsible for incorrect identifications of protozoan trophozoites and cysts and of helminth eggs and larvae. Cyclospora cayetanensis measures approximately 8 to 10 µm and can be easily confused with other coccidia or artifacts, especially if careful measurements are not taken. Without the use of modified acid-fast stains or immunoassay detection methods, a light infection with coccidia will probably be missed; the more normal the stool consistency, the fewer oocysts and more artifacts will be present. One of the most common errors in examining blood smears is the incorrect identification of platelets as parasites. Any laboratory using staining reagents must use good quality control measures to ensure that the solutions do not become contaminated with artifacts or free-living organisms. The human cells most likely to cause problems with identification are the polymorphonuclear leukocytes (PMNs) and the macrophages. Depending on the stain used, small yeast cells can be confused with coccidian oocysts or microsporidial spores.

This is the introductory chapter to the section Mycotic and Parasitic Diseases. Parasitic diseases are historically defined as infectious illnesses caused by unicellular protozoa or multicellular helminths distinct from viral, bacterial, or fungal etiologic agents. Parasites encompass a heterogeneous group of organisms with extremely diverse biologies. Protozoa are usually a few micrometers in size, whereas worms are typically centimeters to meters in length. Tissue-dwelling protozoa are often intracellular parasites. Both protozoan and helminth pathogens have complex life cycles, often with two or more developmental stages present in the host during infection. Immune responses directed against a single stage may be circumvented by parasite differentiation. The diagnosis of mycotic infections cannot always be definitively addressed by culture or histology.

The diversity of eukaryotic microbes is still relatively unexplored, particularly in extreme environments and for the smallest eukaryotes. Estimates of the numbers of clades of eukaryotes vary dramatically and range up to as many as 200 lineages, of which plants, animals, and fungi represent just three clades. This review presents an overview on eukaryotic relationships, describes major innovations within eukaryotes, and illustrates these innovations through examples from major clades. It focuses on representatives of five major clades —alveolates, heterokonts, euglenozoa, opisthokonts, and mycetozoans— as well as a few groups of uncertain taxonomic position—foraminifera, diplomonads, parabasalids. The alveolates are a well-defined clade that emerges from many gene genealogies and includes three major lineages: the ciliates, apicomplexans, and dinoflagellates. The heterokonts, also called stramenopiles, are a diverse group of eukaryotes that include brown algae, diatoms, labyrinthulids, and water molds. The euglenozoa include two major lineages, the euglenids and the kinetoplastids, whose sister status is supported by both ultrastructural and molecular analyses. The opisthokonts include several microbial lineages (e.g., choanoflagellates and microsporidians) as well as two predominantly macroscopic clades (animals and fungi). The mycetozoans, or slime molds, are characterized by complex life cycles that include multicellular fruiting bodies. There are two major types of slime molds: cellular and acellular.

The key to performance of diagnostic medical parasitology procedures is formal training and experience. The majority of diagnostic parasitology procedures can be performed either within the hospital setting or in an offsite location. The majority of physician office laboratories are not involved in diagnostic parasitology testing; however, as more molecular (nonmicroscopic) methods are developed, they may become more widely used in this setting. The specimen most commonly submitted to the diagnostic parasitology laboratory is the stool specimen, and the most commonly performed procedure in parasitology is the ova and parasite (O&P) examination, which comprises three separate protocols: the direct wet mount, the concentration, and the permanent-stained smear. Both flotation and sedimentation methods are available, the most common procedure being the formalin-ethyl acetate sedimentation method (formerly used was the formalin-ether method). Another simplified culture option has been developed for the isolation and identification of Trichomonas vaginalis. This approach has proven to be much more sensitive than the examination of wet preparations alone and has been incorporated into use in many institutions with dramatic increases in the number of positive specimens identified.